The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …

Accurate protein binding structure determination presents a great challenge to both
experiment and theory. Here, in this work, we propose a new DOX protocol which combines …

Free energy differences are calculated for a set of two model host molecules, binding
acetone and methanol. Two active sites of different characteristics were constructed based …

Buried water molecules are ubiquitous in protein structures and are found at the interface of
most protein–ligand complexes. Determining their distribution and thermodynamic effect is a …

Protein–ligand binding is a key biological process at the molecular level. The identification
and characterization of small-molecule binding sites on therapeutically relevant proteins …

The ability to reliably compute accurate protein− ligand binding affinities is crucial to
understanding protein− ligand recognition and to structure-based drug design. A ligand's …

The 3D reference interaction site model (3D‐RISM) of molecular solvation is a powerful tool
for computing the equilibrium thermodynamics and density distributions of solvents, such as …

Predicting solvation free energies and describing the complex water behavior that plays an
important role in essentially all biological processes is a major challenge from the …

This thesis presents the development and application of several computational techniques
to aid in the design and analysis of small molecules and peptides that bind to protein targets …

The important role of water molecules in protein–ligand binding energetics has attracted
wide attention in recent years. A range of computational methods has been developed to …